Isolation of bacterial pathogens from chicken manure, eggshell, and sediments in Changchun City reveal high multidrug-resistant, indices of multiple antibiotic resistance, virulence determinants, and genetic variation.

Pathogens have exhibited the potential for acquiring multiple antibiotic resistance, including beta-lactams, carbapenems and fluoroquinolones. Understanding the transmission dynamics, antimicrobial resistance profile and genetic diversity of the pathogens across different reservoirs is very important. The study sought to isolate bacterial pathogen from chicken manure, egg shell and sediments, profile their antimicrobial resistance patterns, characterize the associated resistance genes and virulence genes while assessing genetic diversity among the recovered isolates. Chicken manure and eggshell samples were collected from local markets, while sediment samples were collected from lakes. The samples were cultured on selective media, isolates were identified by 16S rRNA and species-specific polymerase chain reactions (PCRs), tested for antimicrobial susceptibility test (AST) using 24 antibiotics and screened for resistance, virulence and quorum sensing genes. Multidrug-resistant (MDR) and extensively drug-resistant (XDR) Salmonella enterica serovar Typhimurium, Shigella flexneri, Shigella dysenteriae, Escherichia fergusonii, Citrobacter freundii, Klebsiella pneumoniae subsp. rhinoscleromatis, and Enterobacter cloacae recovered from 65 % of the samples were 100% resistant to amikacin, streptomycin, gentamicin, cefamezin, cephalexin, ampicillin, penicillin, lincomycin, erythromycin and polymyxin B while 85.7% resistant to kanamycin, ciprofloxacin, enrofloxacin, vancomycin cefamezin, cefoperazone, ceftazidime, cefuroxime, ceftriaxone, piperacillin, doxycycline, minocycline, tetracycline, imipenem, and only sulfamethoxazole (71.4 %) was recorded. All the isolates of the bacterial species carried 100 % tetA/B, 85.7 % erm(B), sul I and sul II, blaTEM, strB, and 71.4 % vga(A), strA and qnrC with multiple antibiotic resistance (MAR) ranging from >0.54 - ≥0.96. Virulence genes invA (57.1 %), stn (14.3 %), and quorum sensing gene sdiA (28.6 %) were detected. Positive correlation between phenotypes, resistance genes and virulence markers may indicate active gene flow. High haplotype diversity (87.2 %) and low nucleotide diversity (18%) confirms a dynamic resistome. Chicken manure, egg shells and lake sediments in Changchun act as interconnected reservoirs of clinically relevant MDR and XDR pathogens. Immediate One Health interventions are required to break transmission to humans and livestock.